Structure of PDB 9bbh Chain A Binding Site BS02

Receptor Information
>9bbh Chain A (length=1104) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLR
PVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDI
ITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNK
ELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREK
EFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAP
PIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAM
ETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHA
SIDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEETELMG
FVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWKEPQAKNISV
ASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVACLDITPLGDSN
GLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVF
ACSDRPTVIYSSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLT
IGTIDEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQGTTALRP
SASTQALSSSVSSSEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSC
KLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGA
VYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGD
FILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAE
NAFNLFVCQKDSTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQTPTQGSV
LFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHT
ERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQREATADDLIKVVEEL
TRIH
Ligand information
Ligand IDVVP
InChIInChI=1S/C9H9NO/c1-11-9-4-2-3-8-7(9)5-6-10-8/h2-6,10H,1H3
InChIKeyLUNOXNMCFPFPMO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7COc1cccc2c1cc[nH]2
CACTVS 3.385COc1cccc2[nH]ccc12
ACDLabs 12.01n1ccc2c1cccc2OC
FormulaC9 H9 N O
Name4-methoxy-1H-indole
ChEMBLCHEMBL2018155
DrugBank
ZINCZINC000000407091
PDB chain9bbh Chain A Residue 1204 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB9bbh Co-crystal structure of human DDB1 bound to fragment UB028670
Resolution2.0 Å
Binding residue
(original residue number in PDB)		P69 I88 L145 D146 R147
Binding residue
(residue number reindexed from 1)		P69 I88 L145 D146 R147
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0005515 protein binding
GO:0030674 protein-macromolecule adaptor activity
GO:0044877 protein-containing complex binding
GO:0071987 WD40-repeat domain binding
GO:0097602 cullin family protein binding
GO:0160072 ubiquitin ligase complex scaffold activity
Biological Process
GO:0006281 DNA repair
GO:0006289 nucleotide-excision repair
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006915 apoptotic process
GO:0006974 DNA damage response
GO:0007056 spindle assembly involved in female meiosis
GO:0010498 proteasomal protein catabolic process
GO:0016055 Wnt signaling pathway
GO:0016567 protein ubiquitination
GO:0019076 viral release from host cell
GO:0034644 cellular response to UV
GO:0035234 ectopic germ cell programmed cell death
GO:0042752 regulation of circadian rhythm
GO:0043066 negative regulation of apoptotic process
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0044725 epigenetic programming in the zygotic pronuclei
GO:0045070 positive regulation of viral genome replication
GO:0045722 positive regulation of gluconeogenesis
GO:0045732 positive regulation of protein catabolic process
GO:0046726 positive regulation by virus of viral protein levels in host cell
GO:0048511 rhythmic process
GO:0051093 negative regulation of developmental process
GO:0051702 biological process involved in interaction with symbiont
GO:0070914 UV-damage excision repair
GO:1901990 regulation of mitotic cell cycle phase transition
GO:2000242 negative regulation of reproductive process
Cellular Component
GO:0000781 chromosome, telomeric region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0031464 Cul4A-RING E3 ubiquitin ligase complex
GO:0031465 Cul4B-RING E3 ubiquitin ligase complex
GO:0032991 protein-containing complex
GO:0035861 site of double-strand break
GO:0070062 extracellular exosome
GO:0080008 Cul4-RING E3 ubiquitin ligase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:9bbh, PDBe:9bbh, PDBj:9bbh
PDBsum9bbh
PubMed
UniProtQ16531|DDB1_HUMAN DNA damage-binding protein 1 (Gene Name=DDB1)

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